You Qian, Yang Xiping, Peng Ze, Xu Liping, Wang Jianping
Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China.
Agronomy Department, University of Florida, Gainesville, FL, United States.
Front Plant Sci. 2018 Feb 6;9:104. doi: 10.3389/fpls.2018.00104. eCollection 2018.
Polypoid species play significant roles in agriculture and food production. Many crop species are polyploid, such as potato, wheat, strawberry, and sugarcane. Genotyping has been a daunting task for genetic studies of polyploid crops, which lags far behind the diploid crop species. Single nucleotide polymorphism (SNP) array is considered to be one of, high-throughput, relatively cost-efficient and automated genotyping approaches. However, there are significant challenges for SNP identification in complex, polyploid genomes, which has seriously slowed SNP discovery and array development in polyploid species. Ploidy is a significant factor impacting SNP qualities and validation rates of SNP markers in SNP arrays, which has been proven to be a very important tool for genetic studies and molecular breeding. In this review, we (1) discussed the pros and cons of SNP array in general for high throughput genotyping, (2) presented the challenges of and solutions to SNP calling in polyploid species, (3) summarized the SNP selection criteria and considerations of SNP array design for polyploid species, (4) illustrated SNP array applications in several different polyploid crop species, then (5) discussed challenges, available software, and their accuracy comparisons for genotype calling based on SNP array data in polyploids, and finally (6) provided a series of SNP array design and genotype calling recommendations. This review presents a complete overview of SNP array development and applications in polypoid crops, which will benefit the research in molecular breeding and genetics of crops with complex genomes.
多倍体物种在农业和粮食生产中发挥着重要作用。许多作物物种都是多倍体，如马铃薯、小麦、草莓和甘蔗。基因分型一直是多倍体作物遗传研究中的一项艰巨任务，其发展远远落后于二倍体作物物种。单核苷酸多态性（SNP）阵列被认为是一种高通量、相对经济高效且自动化的基因分型方法。然而，在复杂的多倍体基因组中进行SNP鉴定存在重大挑战，这严重阻碍了多倍体物种中SNP的发现和阵列开发。倍性是影响SNP阵列中SNP质量和SNP标记验证率的一个重要因素，SNP阵列已被证明是遗传研究和分子育种的一个非常重要的工具。在本综述中，我们（1）讨论了SNP阵列在高通量基因分型方面的优缺点，（2）介绍了多倍体物种中SNP检测的挑战及解决方案，（3）总结了多倍体物种SNP选择标准和SNP阵列设计的注意事项，（4）阐述了SNP阵列在几种不同多倍体作物物种中的应用，接着（5）讨论了基于多倍体SNP阵列数据进行基因型检测的挑战、可用软件及其准确性比较，最后（6）提供了一系列SNP阵列设计和基因型检测建议。本综述全面概述了SNP阵列在多倍体作物中的发展和应用，这将有利于复杂基因组作物的分子育种和遗传学研究。
